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LinkageMapView-rendering High-resolution Linkage and QTL Maps

Overview
Journal Bioinformatics
Publisher Oxford University Press
Specialty Biology
Date 2017 Oct 3
PMID 28968706
Citations 89
Authors
Lisa A Ouellette
Robert W Reid
Steven G Blanchard
Cory R Brouwer
Affiliations
Soon will be listed here.
Abstract

Motivation: Linkage and quantitative trait loci (QTL) maps are critical tools for the study of the genetic basis of complex traits. With the advances in sequencing technology over the past decade, linkage map densities have been increasing dramatically, while the visualization tools have not kept pace. LinkageMapView is a free add-on package written in R that produces high resolution, publication-ready visualizations of linkage and QTL maps. While there is software available to generate linkage map graphics, none are freely available, produce publication quality figures, are open source and can run on all platforms. LinkageMapView can be integrated into map building pipelines as it seamlessly incorporates output from R/qtl and also accepts simple text or comma delimited files. There are numerous options within the package to build highly customizable maps, allow for linkage group comparisons, and annotate QTL regions.

Availability And Implementation: https://cran.r-project.org/web/packages/LinkageMapView/.

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References
1.
Voorrips R . MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered. 2002; 93(1):77-8. DOI: 10.1093/jhered/93.1.77. View
2.
Broman K, Wu H, Sen S, Churchill G . R/qtl: QTL mapping in experimental crosses. Bioinformatics. 2003; 19(7):889-90. DOI: 10.1093/bioinformatics/btg112. View
3.
Cavagnaro P, Chung S, Manin S, Yildiz M, Ali A, Alessandro M . Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae. BMC Genomics. 2011; 12:386. PMC: 3162538. DOI: 10.1186/1471-2164-12-386. View
4.
Broman K . R/qtlcharts: interactive graphics for quantitative trait locus mapping. Genetics. 2014; 199(2):359-61. PMC: 4317647. DOI: 10.1534/genetics.114.172742. View